Summary

Target folder: /home/hflavio/Google-drive/workshops_and_presentations/2024-09_OTN/workshop_materials/dataset/2018

Timestamp: 2024-07-24 12:51:11.231463

Number of target tags: 100

Number of listed receivers: 11 (of which 0 had no detections)

Data time range: 2018-03-16 12:14:24 to 2018-08-05 08:11:01 (Europe/Belfast).

Percentage of post-release valid detections: 9.94%

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Study area

Arrays with the same background belong to the same section. Release sites are marked with “R.S.”. Arrays connected with an arrow indicate that the animals can only pass in one direction.

Receiver stations

Station.name Latitude Longitude Array Section Standard.name x.29902 y.29902
Bellisle 55.1095 -6.4454 A1 River St.1 299262 430242
Layde 55.2014 -6.5243 A2 River St.2 294010 440363
Sewage works 55.2104 -6.5317 A3 River St.3 293518 441355
Golf Course 55.2196 -6.5319 A4 River St.4 293484 442379
Runkerry bay 1 55.2216 -6.5416 A5 Sea St.5 292862 442588
Runkerry bay 2 55.2243 -6.5418 A5 Sea St.6 292843 442889
Runkerry bay 3 55.2263 -6.5389 A5 Sea St.7 293023 443115
Runkerry bay 4 55.2280 -6.5361 A5 Sea St.8 293197 443308
Outer bay 1 55.2234 -6.5556 A6 Sea St.9 291967 442770
Outer bay 2 55.2261 -6.5574 A6 Sea St.10 291846 443068
Outer bay 3 55.2285 -6.5553 A6 Sea St.11 291974 443338

Deployments

Receiver Array Station.name Standard.name Start Stop
102881 A5 Runkerry bay 4 St.8 2018-01-01 00:00:01 2019-01-01 00:00:01
102887 A5 Runkerry bay 2 St.6 2018-01-01 00:00:01 2019-01-01 00:00:01
107086 A5 Runkerry bay 3 St.7 2018-01-01 00:00:01 2019-01-01 00:00:01
107087 A1 Bellisle St.1 2018-01-01 00:00:01 2019-01-01 00:00:01
124015 A5 Runkerry bay 1 St.5 2018-01-01 00:00:01 2019-01-01 00:00:01
124258 A2 Layde St.2 2018-01-01 00:00:01 2019-01-01 00:00:01
133182 A3 Sewage works St.3 2018-01-01 00:00:01 2019-01-01 00:00:01
133184 A4 Golf Course St.4 2018-01-01 00:00:01 2019-01-01 00:00:01
546169 A6 Outer bay 2 St.10 2018-01-01 00:00:01 2019-01-01 00:00:01
546170 A6 Outer bay 1 St.9 2018-01-01 00:00:01 2019-01-01 00:00:01
546646 A6 Outer bay 3 St.11 2018-01-01 00:00:01 2019-01-01 00:00:01

Release sites

Station.name Latitude Longitude Array Type Standard.name x.29902 y.29902 n.Wild n.Hatchery
Cross 55.10060 -6.4053 A1 Release Cross 301843 429309 25 25
Trap 55.20271 -6.5231 A3 Release Trap 294084 440510 25 25

Array forward efficiency

Note:
These efficiency calculations do not account for backwards movements. This implies that the total number of animals to have been last seen at a given array may be lower than the displayed below. Please refer to the section survival overview and last seen arrays to find out how many animals were considered to have disappeared per section.
The data used in the tables below is stored in the overall.CJS object. Auxiliary information can also be found in the matrices and arrays objects.
These efficiency values are estimated using the analytical equations provided in the paper “Using mark-recapture models to estimate survival from telemetry data” by Perry et al. (2012). In some situations, more advanced efficiency estimation methods may be required.
You can try running advEfficiency(results$overall.CJS) to obtain beta-drawn efficiency distributions (replace results with the name of the object where you saved the analysis).

Individuals detected and estimated

A1 A2 A3 A4 A5 A6
detected 22 13 34 30 24 7
here plus on peers 13 8 30 24 6 -
not here but on peers 0 0 1 1 1 -
known 22 13 35 31 25 7
estimated 22 13 35 31 28 -

Array efficiency

Note: These values already include any intra-array efficiency estimates that have been requested.

A1 A2 A3 A4 A5 A6
efficiency 100% 100% 96.8% 96% 85.7% -

Warning messages

Warning: Long group names detected. To improve graphic rendering, consider keeping group names under six characters.
Warning: Tag R64K-4332 (1/50) was detected 70831 times at stations less than 1.5 km apart in array 'A5' (St.6, St.7, St.8), over 43.19 days and then disappeared. Could it be inactive?
Warning: Tag R64K-4333 (2/50) was detected 74836 times at stations less than 1.5 km apart in array 'A2' (St.2), over 93.19 days and then disappeared. Could it be inactive?
Warning: Tag R64K-4347 (7/50) jumped through 2 arrays in valid events 2 -> 3 (A2 -> A5).
Warning: Tag R64K-4347 (7/50) was detected 10 times at stations less than 1.5 km apart in array 'A5' (St.7, St.8), over 34.32 days and then disappeared. Could it be inactive?
Warning: Tag R64K-4352 (10/50) was detected 633 times at stations less than 1.5 km apart in array 'A2' (St.2), over 6.22 days and then disappeared. Could it be inactive?
Warning: Tag R64K-4380 (21/50) had an average speed of 1.32 m/s from valid event 5 to 6 (A5 -> A6).
Warning: Tag R64K-4396 (32/50) was detected in an array that is not after its release site! Opening relevant data for inspection.
Expected first array: A3
Warning: Tag R64K-4404 (35/50) was detected 5076 times at stations less than 1.5 km apart in array 'A4' (St.4), over 5.18 days and then disappeared. Could it be inactive?
Warning: Tag R64K-4415 (41/50) had an average speed of 0.75 m/s from valid event 6 to 7 (A6 -> A5).

User comments

R64K-4347   Tough one. To be conservative, consider it survived.
R64K-4352   Does not spend much time on array, but keeps pinging repeatedly. Removing trailing events.
R64K-4380   Extremely fast speed between A5 and A6. Does not impact fate, so I will leave it all in.
R64K-4396   Only detected upstream of release, at impossible site. Rendered invalid.

Biometric graphics

Note:
The data used in this graphic is the data present in the biometrics.csv file.

Section Survival

Note:
The data used in this table and graphic is stored in the section.overview object.
Total Disap..in.River Migrated.to.Sea Disap..in.Sea Succeeded
Hatchery 50 35 15 3 12
Wild 50 34 16 3 13

Last Seen Arrays

Note:
The data used in this graphic is stored in the status.df object (‘Very.last.array’ column).

Progression

Zoom in or open the figure in a new tab to clearly read the text within each circle.

Note:
The progression calculations do not account for backwards movements. This implies that the total number of animals to have been last seen at a given array may be lower than the displayed below. Please refer to the section survival overview and last seen arrays to find out how many animals were considered to have disappeared per section.
The data used in this graphic is stored in the overall.CJS object, and the data used in the tables is stored in the group.overview object. You can find detailed progressions per release site in the release.overview object.

Group: Wild

Release A1 A2 A3 A4 A5 A6
detected 50 12 8 17 15 12 2
here plus on peers - 8 6 15 12 1 -
not here but on peers - 0 0 1 1 1 -
known 50 12 8 18 16 13 2
estimated - 12 8 18 16 14 -
difference - 0 0 0 0 1 -

Group: Hatchery

Release A1 A2 A3 A4 A5 A6
detected 50 10 5 17 15 12 5
here plus on peers - 5 2 15 12 5 -
not here but on peers - 0 0 0 0 0 -
known 50 10 5 17 15 12 5
estimated - 10 5 18 16 14 -
difference - 0 0 1 1 2 -

Time of arrival at each Array

Note:
Coloured lines on the outer circle indicate the mean value for each group and the respective ranges show the standard error of the mean. Each group’s bars sum to 100%. The number of data points in each group is presented between brackets in the legend of each pannel.
You can replicate these graphics and edit them as needed using the plotTimes() function.
The data used in these graphics is stored in the times object.
To obtain reports with the legacy linear circular scale, run options(actel.circular.scale = "linear") before running your analyses.

/tmp/Rtmpe00LlA/actel_report_auxiliary_files/circular_svg_print_failure_bounce_back.png /tmp/Rtmpe00LlA/actel_report_auxiliary_files/circular_svg_print_failure_bounce_back.png /tmp/Rtmpe00LlA/actel_report_auxiliary_files/circular_svg_print_failure_bounce_back.png

Dotplots

Note:
The top 10% of the values for each panel are marked in red.
The bottom 10% of the values for each panel are marked in blue.
The columns starting with “To” should be read as either “Average time to …” or “Average speed to …”, depending on the unit used. The columns starting with “In” should be read as “Total time in …”. These reductions were made to keep the column headers as short as possible.
The data used in these graphics is stored in the status.df object.

Individual detection plots

Note:
You can choose to plot detections by station or by array using the detections.y.axis argument.
The detections are coloured by section. The vertical black dashed line shows the time of release. The vertical grey dashed lines show the assigned moments of entry and exit for each study area section. The full dark-grey line shows the movement events considered valid, while the dashed dark-grey line shows the movement events considered invalid.
Manually edited tag detections are highlighted with yellow graphic borders.
Manually overridden tag detections are highlighted with red graphic borders.
The arrays have been aligned by section, following the order provided either in the spatial input or the section.order argument.
You can replicate these graphics and edit them as needed using the plotDetections() function.
You can also see the movement events of multiple tags simultaneously using the plotMoves() function.
The data used in these graphics is stored in the detections and movements objects (and respective valid counterparts).

Full log

Actel R package report.
Version: 1.3.0.9007

Target folder: /home/hflavio/Google-drive/workshops_and_presentations/2024-09_OTN/workshop_materials/dataset/2018
Timestamp: 2024-07-24 12:51:11.231463
Function: migration()

M: 'report' option has been activated.
M: Importing data. This process may take a while.
M: No Code.space column was found in the biometrics. Assigning code spaces based on detections.
Warning: Long group names detected. To improve graphic rendering, consider keeping group names under six characters.
M: Number of target tags: 100.
M: Matching detections with deployment periods.
M: Number of ALS: 11 (of which 0 had no detections)
M: Data time range: 2018-03-16 12:14:24 to 2018-08-05 08:11:01 (Europe/Belfast).
M: File 'distances.csv' found, activating speed calculations.
M: Data successfully imported!
M: Creating movement records for the valid tags.
M: Checking movement events quality.
Warning: Tag R64K-4332 (1/50) was detected 70831 times at stations less than 1.5 km apart in array 'A5' (St.6, St.7, St.8), over 43.19 days and then disappeared. Could it be inactive?
M: 26 movement event(s) from tag R64K-4332 were rendered invalid per user command.
Warning: Tag R64K-4333 (2/50) was detected 74836 times at stations less than 1.5 km apart in array 'A2' (St.2), over 93.19 days and then disappeared. Could it be inactive?
M: 122 movement event(s) from tag R64K-4333 were rendered invalid per user command.
Warning: Tag R64K-4347 (7/50) jumped through 2 arrays in valid events 2 -> 3 (A2 -> A5).
Warning: Tag R64K-4347 (7/50) was detected 10 times at stations less than 1.5 km apart in array 'A5' (St.7, St.8), over 34.32 days and then disappeared. Could it be inactive?
M: Movement event(s) 4, 5, 6, 7, 8, 9, 10, 11, 12 from tag R64K-4347 were rendered invalid per user command.
Warning: Tag R64K-4352 (10/50) was detected 633 times at stations less than 1.5 km apart in array 'A2' (St.2), over 6.22 days and then disappeared. Could it be inactive?
M: Movement event(s) 3, 4, 5, 6, 7, 8, 9, 10, 11 from tag R64K-4352 were rendered invalid per user command.
Warning: Tag R64K-4380 (21/50) had an average speed of 1.32 m/s from valid event 5 to 6 (A5 -> A6).
Warning: Tag R64K-4396 (32/50) was detected in an array that is not after its release site! Opening relevant data for inspection.
Expected first array: A3
M: ALL movement events from tag R64K-4396 were rendered invalid per user command.
Warning: Tag R64K-4404 (35/50) was detected 5076 times at stations less than 1.5 km apart in array 'A4' (St.4), over 5.18 days and then disappeared. Could it be inactive?
M: Movement event(s) 3, 4 from tag R64K-4404 were rendered invalid per user command.
Warning: Tag R64K-4415 (41/50) had an average speed of 0.75 m/s from valid event 6 to 7 (A6 -> A5).
M: Compiling and checking section movements for the valid tags.
M: Filtering valid array movements.
M: Filtering valid section movements.
M: Compiling migration timetable.
M: Compiling summary information tables.
M: Calculating array efficiency.
M: Saving results as 'actel_migration_results.RData'.
M: Producing the report.
M: Drawing individual detection graphics.
M: Analysis completed!

-------------------
User comments:
-------------------
R64K-4347: Tough one. To be conservative, consider it survived.
R64K-4352: Does not spend much time on array, but keeps pinging repeatedly. Removing trailing events.
R64K-4380: Extremely fast speed between A5 and A6. Does not impact fate, so I will leave it all in.
R64K-4396: Only detected upstream of release, at impossible site. Rendered invalid.
-------------------
User interventions:
-------------------
y # save strays?
y # invalidate/expand moves in R64K-4332?
10:35
y # confirm?
n # invalidate more?
y # invalidate/expand moves in R64K-4333?
3:124
y # confirm?
n # invalidate more?
comment # on R64K-4347
Tough one. To be conservative, consider it survived.
y # invalidate/expand moves in R64K-4347?
4:12
y # confirm?
n # invalidate more?
comment # on R64K-4352
Does not spend much time on array, but keeps pinging repeatedly. Removing trailing events.
y # invalidate/expand moves in R64K-4352?
3:11
y # confirm?
n # invalidate more?
comment # on R64K-4380
Extremely fast speed between A5 and A6. Does not impact fate, so I will leave it all in.
n # invalidate/expand moves in R64K-4380?
comment # on R64K-4396
Only detected upstream of release, at impossible site. Rendered invalid.
y # invalidate/expand moves in R64K-4396?
1:3
y # confirm?
y # invalidate/expand moves in R64K-4404?
3, 4
y # confirm?
n # invalidate more?
n # invalidate/expand moves in R64K-4415?
y # save results?
-------------------
Migration function call:
-------------------
migration(tz = 'Europe/Belfast', section.order = NULL, datapack = NULL, success.arrays = c('A5', 'A6'), max.interval = 60, min.total.detections = 2, min.per.event = c(1, 1), start.time = NULL, stop.time = NULL, speed.method = 'last to first', speed.warning = 0.7, speed.error = 0.7, jump.warning = 2, jump.error = 3, inactive.warning = 3, inactive.error = 5, exclude.tags = NULL, override = NULL, report = TRUE, auto.open = TRUE, discard.orphans = FALSE, discard.first = NULL, save.detections = FALSE, if.last.skip.section = TRUE, replicates = NULL, disregard.parallels = TRUE, GUI = 'needed', save.tables.locally = FALSE, print.releases = TRUE, detections.y.axis = 'auto')
-------------------

Index:

Summary Study area Stations Deployments Release sites Array efficiency Warnings Comments Biometrics Section survival Last seen Progression Arrival times Dotplots Individual detections Full log